1Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG). Dr. Aiguader 88, Barcelona 08003, Spain. 2Universitat Pompeu Fabra (UPF). 08003Barcelona, Spain. 3 INRA, UR1052 GAFL, CS 60094, F- 84140 Montfavet Cedex, France. 4Mediterranean Centre for Marine and Environmental Research (ICM-CSIC) Pg. Maritim de la Barceloneta 37-49, 08003 Barcelona,
Spain, 5Mediterranean Institute of Oceanography (MIO) Aix-Marseille University, CNRS/INSU, IRD, UM 110, 13288 Marseille, France, 6Biology Department, Amherst College, Amherst MA 01002, USA. 7CNRS,
UMR 8079 Ecologie, Systématique et Evolution, Bâtiment 360, F-91405,
Orsay, France.8UMR 8079 Université Paris Sud, Ecologie,
Systématique et Evolution, Bâtiment 360,
F-91405, Orsay, France.9 Institució Catalana de Recerca i Estudis
Avancats. Pg. Lluís
Companys 23, 08010, Barcelona, Spain.
From their origin as an early alpha
proteobacterial endosymbiont to their current state as cellular
genomic reorganization has taken place in the
mitochondria of all main eukaryotic lineages. So far, most studies have
on plant and animal mitochondrial genomes (mtDNA)
but fungi provide new opportunities to study highly differentiated
Here we analyzed 38 complete fungal mitochondrial
genomes to investigate the evolution of mtDNA gene order among fungi. In
particular, we looked for evidence of
non-homologous intrachromosomal recombination and investigated the
dynamics of gene
rearrangements. We analyzed the effect that
introns, intronic open reading frames (ORFs) and repeats may have on
Additionally, we asked whether the distribution of
transfer RNAs (tRNAs) evolves independently to that of mt protein-coding
genes. We found that fungal mitochondrial genomes
display remarkable variation between and within the major fungal phyla
terms of gene order, genome size, composition of
intergenic regions, and presence of repeats, introns and associated
Our results support previous evidence for the
presence of mitochondrial recombination in all fungal phyla, a process
lacking in most Metazoa. Overall, the patterns of
rearrangements may be explained by the combined influences of
(i.e., most likely non-homologous, intrachromosomal), accumulated repeats, especially at intergenic regions, and to a lesser extent,
mobile element dynamics.
مقاله 2013: فیلوژنی و ژنیتک جمعیت بدون انجام هم ردیفی توالی ها
Alignment-free phylogenetics and population genetics
Phylogenetics and population genetics are
central disciplines in evolutionary biology. Both are based on
today usually DNA sequences. These have become so
plentiful that alignment-free sequence comparison is of growing
in the race between scientists and sequencing
machines. In phylogenetics, efficient distance computation is the major
of alignment-free methods. A distance measure
should reflect the number of substitutions per site, which underlies
alignment-based phylogeny reconstruction.
Alignment-free distance measures are either based on word counts or on
and I apply examples of both approaches to
simulated and real data to assess their accuracy and efficiency. While
reconstruction is based on the number of
substitutions, in population genetics, the distribution of mutations
along a sequence
is also considered. This distribution can be
explored by match lengths, thus opening the prospect of alignment-free
Toward genome-enabled mycology
David S. Hibbett1
Biology Department, Clark University, Worcester, Massachusetts 01610
Jason E. Stajich
Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521
Joseph W. Spatafora
+ Author Affiliations
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.
Fungi play a central
role in both ecosystems and human societies. This is in part because
they have adopted a large diversity of life history traits to conquer a
wide variety of ecological niches. Here, I review recent fungal genomics
studies that explored the molecular origins and the adaptive
significance of this diversity. First, macro-ecological genomics studies
revealed that fungal genomes were highly remodelled during their
evolution. This remodelling, in terms of genome organization and size,
occurred through the proliferation of non-coding elements, gene
compaction, gene loss and the expansion of large families of adaptive
genes. These features vary greatly among fungal clades, and are
correlated with different life history traits such as multicellularity,
pathogenicity, symbiosis, and sexual reproduction. Second,
micro-ecological genomics studies, based on population genomics,
experimental evolution and quantitative trait loci approaches, have
allowed a deeper exploration of early evolutionary steps of the above
adaptations. Fungi, and especially budding yeasts, were used intensively
to characterize early mutations and chromosomal rearrangements that
underlie the acquisition of new adaptive traits allowing them to conquer
new ecological niches and potentially leading to speciation. By
uncovering the ecological factors and genomic modifications that
underline adaptation, these studies showed that Fungi are powerful
models for ecological genomics (eco-genomics), and that this approach,
so far mainly developed in a few model species, should be expanded to
the whole kingdom.
جدیدترین طبقه بندی قارچ ها، آخرین طبقه بندی قارچ ها
هم اکنون (2013) قارچ ها در هشت (یا 9) شاخه یا فایلوم قرار می گیرند. اخیرا اضافه شدن شاخه نهمی به نام کریپتومایکوتا (Cryptomycota) به قارچ ها پیشنهاد شده است، که بر خلاف سایر قارچ های معمول در دیواره فاقد کیتین هستند.
Department of Biological Sciences; Louisiana State University; Baton Rouge, Louisiana 70803 USA
Received for publication 10 August 2010.
Accepted for publication 19 January 2011.
• Premise of the study: Fungi are
major decomposers in certain ecosystems and essential associates of
many organisms. They provide enzymes and drugs
and serve as experimental organisms. In 1991, a
landmark paper estimated that there are 1.5 million fungi on the Earth.
only 70000 fungi had been described at that time,
the estimate has been the impetus to search for previously unknown
Fungal habitats include soil, water, and organisms
that may harbor large numbers of understudied fungi, estimated to
plants by at least 6 to 1. More recent estimates
based on high-throughput sequencing methods suggest that as many as 5.1
fungal species exist.
• Methods: Technological advances make it possible to apply molecular methods to develop a stable classification and to discover and
identify fungal taxa.
• Key results: Molecular methods
have dramatically increased our knowledge of Fungi in less than 20
years, revealing a monophyletic kingdom
and increased diversity among early-diverging
lineages. Mycologists are making significant advances in species
but many fungi remain to be discovered.
• Conclusions: Fungi are
essential to the survival of many groups of organisms with which they
form associations. They also attract attention
as predators of invertebrate animals, pathogens of
potatoes and rice and humans and bats, killers of frogs and crayfish,
of secondary metabolites to lower cholesterol, and
subjects of prize-winning research. Molecular tools in use and under
can be used to discover the world’s unknown fungi
in less than 1000 years predicted at current new species acquisition
مقاله 2013 در ارتباط با تاکسونومی قارچ ها: ارتباط نزدیک اعضای شاخه کریپتومایکوتا و میکروسپوریدیا بر اساس شواهد فیزیولوژیکی و فیلوژنتیکی
Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia
•Phylogenomics demonstrates Rozella and microsporidia are closely related early fungi
•The Rozella genome encodes four chitin synthases, including one with a myosin domain
•The Rozella mitochondrial genome shows evidence of rapid evolution and degeneration
•The Rozella nuclear genome lacks a large number of genes for primary metabolism
Fungi grow within their food, externally digesting it and absorbing nutrients across a semirigid chitinous cell wall. Members of the new phylum Cryptomycota were proposed to represent intermediate fungal forms, lacking a chitinous cell wall during feeding and known almost exclusively from ubiquitous environmental ribosomal RNA sequences that cluster at the base of the fungal tree [1 and 2]. Here, we sequence the first Cryptomycotan genome (the water mold endoparasite Rozella allomycis) and unite the Cryptomycota with another group of endoparasites, the microsporidia, based on phylogenomics and shared genomic traits. We propose that Cryptomycota and microsporidia share a common endoparasitic ancestor, with the clade unified by a chitinous cell wall used to develop turgor pressure in the infection process [ 3 and 4]. Shared genomic elements include a nucleotide transporter that is used by microsporidia for stealing energy in the form of ATP from their hosts . Rozella harbors a mitochondrion that contains a very rapidly evolving genome and lacks complex I of the respiratory chain. These degenerate features are offset by the presence of nuclear genes for alternative respiratory pathways. The Rozella proteome has not undergone major contraction like microsporidia; instead, several classes have undergone expansion, such as host-effector, signal-transduction, and folding proteins.
Tip Growth in Filamentous Fungi: A Road Trip to the Apex
Annual Review of Microbiology
Review in Advance first posted online on June 28, 2013.
Fungal hyphae extend by apical growth. This process involves the polarized traffic of secretory vesicles to the Spitzenkörper (SPK) and their subsequent distribution to specific domains of the plasma membrane, where they fuse to provide all the enzymes and material needed for cell wall expansion. Endocytic recycling and localized translation of specific mRNA splay an important role in hyphal apical growth. The traffic of vesicular carriers from synthesis sites to their destinations is coordinated by the combined action of coats, tethers, Rab GTPases, motors, and SNAREs in a mechanism that is just beginning to be understood. Only recently has it been confirmed that the different-sized vesicles present at the SPK contain distinct cell wall biosynthetic activities and are distributed in a stratified manner.
Submitted to: Mycotaxon Publication Type: Peer Reviewed Journal Publication Acceptance Date: August 19, 2012 Publication Date: N/A
Interpretive Summary: This manuscript provides an overall reclassification of fungi from the order Entomophthorales in order to facilitate a set of future studies on the phylogeny of these fungi. This reclassification incorporates more recent gene-based information with the overall biology of these fungi. A series of difficulties in the treatments of the genera Basidiobolus and Neozygites in this new classification are discussed and points out the need to incorporate more than sequence-based data. This reclassification replaces the previous traditionally based classification of these fungi in one order and six families with one new phylum divided into three classes while retaining the previously defined family structure.
Technical Abstract: One result of the recent phylogenetically based rejection of the phylum Zygomycota was the description of the subphylum Entomophthoromycotina (not assigned to any phylum) for fungi traditionally treated in the order Entomophthorales. More extensive gene-based analyses of these fungi suggest that they represent a monophyletic lineage distinct from all other fungi that deserves now to be recognized at the level of a new fungal phylum. These molecular data and further analyses of more traditional taxonomic criteria lead to this reclassification that still treats these fungi in six families, but that recognizes the new classes Basidiobolomycetes, Neozygitomycetes, and Entomophthoromycetes as well as the new order Neozygitales. Ballocephala and Zygnemomyces are rejected from Entomophthorales (Meristacraceae) and should be reclassified among the Kickxellomycotina.
Duke University, Department of Biology, Durham, NC 27708-90338, USA. Andrii.Gryganskyi@gmail.com
The Entomophthoromycota is a ubiquitous group of fungi best known as pathogens of a wide variety of economically important insect pests, and other soil invertebrates. This group of fungi also includes a small number of parasites of reptiles, vertebrates (including humans), macromycetes, fern gametophytes, and desmid algae, as well as some saprobic species. Here we report on recent studies to resolve the phylogenetic relationships within the Entomophthoromycota and to reliably place this group among other basal fungal lineages. Bayesian Interference (BI) and Maximum Likelihood (ML) analyses of three genes (nuclear 18S and 28S rDNA, mitochondrial 16S, and the protein-coding RPB2) as well as non-molecular data consistently and unambiguously identify 31 taxa of Entomophthoromycota as a monophyletic group distinct from other Zygomycota and flagellated fungi. Using the constraints of our multi-gene dataset we constructed the most comprehensive rDNA phylogeny yet available for Entomophthoromycota. The taxa studied here belong to five distinct, well-supported lineages. The Basidiobolus clade is the earliest diverging lineage, comprised of saprobe species of Basidiobolus and the undescribed snake parasite Schizangiella serpentis nom. prov. The Conidiobolus lineage is represented by a paraphyletic grade of trophically diverse species that include saprobes, insect pathogens, and facultative human pathogens. Three well supported and exclusively entomopathogenic lineages in the Entomophthoraceae center around the genera Batkoa, Entomophthora and Zoophthora, although several genera within this crown clade are resolved as non-monophyletic. Ancestral state reconstruction suggests that the ancestor of all Entomophthoromycota was morphologically similar to species of Conidiobolus. Analyses using strict, relaxed, and local molecular clock models documented highly variable DNA substitution rates among lineages of Entomophthoromycota. Despite the complications caused by different rates of molecular evolution among lineages, our dating analysis indicates that the Entomophthoromycota originated 405±90 million years ago. We suggest that entomopathogenic lineages in Entomophthoraceae probably evolved from saprobic or facultatively pathogenic ancestors during or shortly after the evolutionary radiation of the arthropods.
aLos Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
bInstitute of Information Management, National Cheng Kung University, Tainan City, Taiwan, Republic of China
cDepartment of Biological Sciences, Western Illinois University, Macomb, Illinois, USA
dDepartment of Biology, University of New Mexico, Albuquerque, New Mexico, USA
Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project (http://rdp.cme.msu.edu/classifier/classifier.jsp).
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
Edited* by Daniel H. Janzen, University of Pennsylvania, Philadelphia, PA, and approved February 24, 2012 (received for review October 18, 2011)
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
No jacket required – new fungal lineage defies dress code
Recently described zoosporic fungi lack a cell wall during trophic phase
Timothy Y. James1,*,
Mary L. Berbee2,*
Analyses of environmental DNAs have provided tantalizing evidence for “rozellida” or “cryptomycota”, a clade of mostly undescribed and deeply diverging aquatic fungi. Here, we put cryptomycota into perspective through consideration of Rozella, the only clade member growing in culture. This is timely on account of the publication in Nature of the first images of uncultured cryptomycota from environmental filtrates, where molecular probes revealed non-motile cyst-like structures and motile spores, all lacking typical fungal chitinous cell walls. Current studies of Rozella can complement these fragmentary observations from environmental samples. Rozella has a fungal-specific chitin synthase and its resting sporangia have walls that appear to contain chitin. Cryptomycota, including Rozella, lack a cell wall when absorbing food but like some other fungi, they may have lost their “dinner jacket” through convergence. Rather than evolutionary intermediates, the cryptomycota may be strange, divergent fungi that evolved from an ancestor with a nearly complete suite of classical fungal-specific characters.
School of Biosciences, University of Exeter, Exeter EX4 4QD, UK;
The recently proposed new phylum name Cryptomycota phyl. nov. is validly published in order to facilitate its use in future discussions of the ecology, biology, and phylogenetic relationships of the constituent organisms. This name is preferred over the previously tentatively proposed "Rozellida" as new data suggest that the life-style and morphology of Rozella is not representative of the large radiation to which it and other Cryptomycota belong. Furthermore, taxa at higher ranks such as phylum are considered better not based on individual names of included genera, but rather on some special characteristics - in this case the cryptic nature of this group and that they were initially revealed by molecular methods rather than morphological discovery. If the group were later viewed as a member of a different kingdom, the name should be retained to indicate its fungal affinities, as is the practice for other fungal-like protist groups.
مقاله ۲۰۱۲: ده پاتوژن قارچی برتر در بیماری شناسی گیاهی مولکولی
The Top 10 fungal pathogens in molecular plant pathology
The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a ‘Top 10’ based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.
Table 1. Top 10 fungal plant pathogens.
Author of fungal description
The table represents the ranked list of fungi as voted for by plant mycologists associated with the journal Molecular Plant Pathology.